I just checkout your site for a few minutes, so I don`t have all the answers for you but I`ll bet I send you in the right direction. Mostly cause it happened to one of my sites too. When you use a platform like yours to create dynamically generated pages, there are few things you`re going to have to do. I`ll try to keep the cookies on the lower shelf here so as not to cloud the water with muck.
The reason you saw Google index all those pages was because it`s search spider saw that there was a bunch of new content after you made the change to your new platform. As you said that was the good part. WHoa look at all that new stuff!
Bad part...Dynamically produce pages are not real pages as in html pages that people labor over for days. But it`s actually a template page that has various control sections in it that hit the specific product information on your sql server and draws it into the page composition. Here`s the part people tend to mis. That is actually one page...lets call it productdetail.aspx. So after Google crawled it a couple times and started trying to index the content further, it actually started seeing it as the same page with "slightly" different content. At which time it did its Google thing and said "Duplicate Content" and whacked it from your indexed pages.
But don`t worry all is not lost. Contact whoever it was that set this up for you and make a few mods to the way the page controls pull information into the product detail page and if you have category pages or catalog pages.(some people call them different things) Those pages need to be dealt with too. They may need to add some new fields to your database. Of course that depends on what you have there now. And then make a few code changes to the controll code files (sometimes called code behind file or behind code)
Have the page name control deliver the product name to the <Meta Name> Tag.
If you use long and short product descriptions, deliver the short description to the <Meta description> tag.
If possible create a new control for the product detail page to include an <H1> tag. This can be used as a product headline above the copy or as a short statement at the top of the page.
Make sure there is a keyword field in your database and that those keywords are delivered to the <Meta Keyword> tag.
All of these fields need to reflect the appropriate keywords, starting with the product name, and they need to be as unique as possible.
Next if you don`t have one already setup a Google xml sitemap.
Getting those indexed pages back is definately important, and the bad news is that there is still some grunt work to do. However with type of platform, in the future things will go much smoother. Everytime you add a new product to the database those fields will be there and it won`t be such a big deal. You just have to set it up so that Gogle sees those pages as individuals not clones.
Don`t worry, once you set it up right, the pages will reappear...pesto! after about 2 to 3 weeks.
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